data_19024 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; single G-bulge in a conserved regulatory region of the HEV genome ; _BMRB_accession_number 19024 _BMRB_flat_file_name bmr19024.str _Entry_type original _Submission_date 2013-02-11 _Accession_date 2013-02-11 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lescrinier Eveline . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count assigned_chemical_shifts 1 stop_ loop_ _Data_type _Data_type_count "1H chemical shifts" 120 "13C chemical shifts" 137 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2014-03-03 original author . stop_ _Original_release_date 2014-03-03 save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title 'Binding of a naphtyridine analogue to the single G-bulge in a conserved regulatory region of the HEV genome' _Citation_status 'in preparation' _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID ? loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Lescrinier Eveline . . stop_ _Journal_abbreviation 'Not known' _Journal_volume . _Journal_issue . _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first . _Page_last . _Year . _Details . save_ ################################## # Molecular system description # ################################## save_assembly _Saveframe_category molecular_system _Mol_system_name 'single G-bulge in a conserved regulatory region of the HEV genome' _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label RNA $RNA stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state ? _System_paramagnetic no _System_thiol_state . _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_RNA _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class RNA _Name_common RNA _Molecular_mass 132.116 _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 17 _Mol_residue_sequence GGAAUCGAAAGAUGUCC loop_ _Residue_seq_code _Residue_author_seq_code _Residue_label 1 1 G 2 2 G 3 3 A 4 4 A 5 5 U 6 6 C 7 7 G 8 8 A 9 9 A 10 10 A 11 11 G 12 12 A 13 13 U 14 14 G 15 15 U 16 16 C 17 17 C stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date . save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $RNA . . . . HEV HEV stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $RNA 'chemical synthesis' . HEV HEV . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA 1 mM 'natural abundance' D2O 100 % 'natural abundance' stop_ save_ save_sample_2 _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $RNA 1 mM 'natural abundance' DHO 90 % 'natural abundance' D2O 10 % 'natural abundance' stop_ save_ ############################ # Computer software used # ############################ save_X-PLOR_NIH _Saveframe_category software _Name 'X-PLOR NIH' _Version . loop_ _Vendor _Address _Electronic_address 'Schwieters, Kuszewski, Tjandra and Clore' . . stop_ loop_ _Task 'structure solution' stop_ _Details . save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_spectrometer_1 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 500 _Details . save_ save_spectrometer_2 _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model Avance _Field_strength 600 _Details cryoprobe save_ ############################# # NMR applied experiments # ############################# save_2D_1H-13C_HSQC_aliphatic_1 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aliphatic' _Sample_label $sample_1 save_ save_2D_1H-13C_HSQC_aromatic_2 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-13C HSQC aromatic' _Sample_label $sample_1 save_ save_2D_1H-1H_TOCSY_3 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H TOCSY' _Sample_label $sample_1 save_ save_2D_DQF-COSY_4 _Saveframe_category NMR_applied_experiment _Experiment_name '2D DQF-COSY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_5 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_6 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_7 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_1 save_ save_2D_1H-1H_NOESY_8 _Saveframe_category NMR_applied_experiment _Experiment_name '2D 1H-1H NOESY' _Sample_label $sample_2 save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH pressure 1 . atm temperature 288 . K stop_ save_ save_sample_conditions_2 _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 7 . pH temperature 273 . K stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference_1 _Saveframe_category chemical_shift_reference _Details . loop_ _Mol_common_name _Atom_type _Atom_isotope_number _Atom_group _Chem_shift_units _Chem_shift_value _Reference_method _Reference_type _External_reference_sample_geometry _External_reference_location _External_reference_axis _Indirect_shift_ratio DSS H 1 'methyl protons' ppm 0.00 internal direct . . . 1.000000000 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chem_shift_list_1 _Saveframe_category assigned_chemical_shifts _Details . loop_ _Experiment_label '2D 1H-1H TOCSY' '2D DQF-COSY' '2D 1H-1H NOESY' stop_ loop_ _Sample_label $sample_1 stop_ _Sample_conditions_label $sample_conditions_1 _Chem_shift_reference_set_label $chemical_shift_reference_1 _Mol_system_component_name RNA _Text_data_format . _Text_data . loop_ _Atom_shift_assign_ID _Residue_author_seq_code _Residue_seq_code _Residue_label _Atom_name _Atom_type _Chem_shift_value _Chem_shift_value_error _Chem_shift_ambiguity_code 1 1 1 G H1' H 5.717 0.000 . 2 1 1 G H2' H 4.864 0.000 . 3 1 1 G H3' H 4.532 0.000 . 4 1 1 G H4' H 4.318 0.000 . 5 1 1 G H5' H 3.883 0.000 . 6 1 1 G H5'' H 3.990 0.000 . 7 1 1 G H8 H 7.971 0.000 . 8 1 1 G C1' C 89.852 0.000 . 9 1 1 G C2' C 72.518 0.000 . 10 1 1 G C3' C 71.026 0.000 . 11 1 1 G C4' C 81.604 0.000 . 12 1 1 G C5 C 115.964 0.000 . 13 1 1 G C5' C 59.520 0.000 . 14 1 1 G C8 C 135.690 0.000 . 15 2 2 G H1' H 5.891 0.000 . 16 2 2 G H2' H 4.729 0.000 . 17 2 2 G H3' H 4.642 0.000 . 18 2 2 G H4' H 4.517 0.000 . 19 2 2 G H5' H 4.151 0.000 . 20 2 2 G H5'' H 4.531 0.000 . 21 2 2 G H8 H 7.467 0.000 . 22 2 2 G C1' C 89.862 0.000 . 23 2 2 G C2' C 72.641 0.000 . 24 2 2 G C3' C 69.908 0.000 . 25 2 2 G C4' C 79.298 0.000 . 26 2 2 G C5' C 62.247 0.000 . 27 2 2 G C8 C 133.719 0.000 . 28 3 3 A H1' H 5.901 0.000 . 29 3 3 A H2 H 7.450 0.000 . 30 3 3 A H2' H 4.760 0.000 . 31 3 3 A H3' H 4.551 0.000 . 32 3 3 A H4' H 4.549 0.000 . 33 3 3 A H5' H 4.146 0.000 . 34 3 3 A H5'' H 4.523 0.000 . 35 3 3 A H8 H 7.563 0.000 . 36 3 3 A C1' C 90.508 0.000 . 37 3 3 A C2 C 150.338 0.000 . 38 3 3 A C2' C 72.627 0.000 . 39 3 3 A C3' C 70.221 0.000 . 40 3 3 A C4 C 145.698 0.000 . 41 3 3 A C4' C 79.412 0.000 . 42 3 3 A C5' C 62.827 0.000 . 43 3 3 A C6 C 154.431 0.000 . 44 3 3 A C8 C 136.214 0.000 . 45 4 4 A H1' H 5.687 0.000 . 46 4 4 A H2 H 7.767 0.000 . 47 4 4 A H2' H 4.373 0.000 . 48 4 4 A H3' H 4.574 0.000 . 49 4 4 A H4' H 4.471 0.000 . 50 4 4 A H8 H 7.735 0.000 . 51 4 4 A C1' C 89.954 0.000 . 52 4 4 A C2 C 151.156 0.000 . 53 4 4 A C2' C 72.545 0.000 . 54 4 4 A C3' C 69.595 0.000 . 55 4 4 A C4 C 145.860 0.000 . 56 4 4 A C4' C 79.184 0.000 . 57 4 4 A C5 C 118.026 0.000 . 58 4 4 A C6 C 155.403 0.000 . 59 4 4 A C8 C 136.033 0.000 . 60 5 5 U H1' H 5.417 0.000 . 61 5 5 U H2' H 4.163 0.000 . 62 5 5 U H3' H 4.447 0.000 . 63 5 5 U H4' H 4.363 0.000 . 64 5 5 U H5 H 5.131 0.000 . 65 5 5 U H5' H 4.051 0.000 . 66 5 5 U H5'' H 4.495 0.000 . 67 5 5 U H6 H 7.628 0.000 . 68 5 5 U C1' C 90.180 0.000 . 69 5 5 U C2 C 149.633 0.000 . 70 5 5 U C2' C 72.585 0.000 . 71 5 5 U C3' C 68.915 0.000 . 72 5 5 U C4 C 165.305 0.000 . 73 5 5 U C4' C 78.766 0.000 . 74 5 5 U C5 C 99.968 0.000 . 75 5 5 U C5' C 61.214 0.000 . 76 5 5 U C6 C 138.810 0.000 . 77 6 6 C H1' H 5.608 0.000 . 78 6 6 C H2' H 4.395 0.000 . 79 6 6 C H3' H 4.360 0.000 . 80 6 6 C H5 H 5.454 0.000 . 81 6 6 C H5' H 4.069 0.000 . 82 6 6 C H5'' H 4.450 0.000 . 83 6 6 C H6 H 7.615 0.000 . 84 6 6 C C1' C 90.617 0.000 . 85 6 6 C C2' C 72.941 0.000 . 86 6 6 C C3' C 68.942 0.000 . 87 6 6 C C5 C 95.233 0.000 . 88 6 6 C C5' C 61.668 0.000 . 89 6 6 C C6 C 137.444 0.000 . 90 7 7 G H1' H 5.601 0.000 . 91 7 7 G H2' H 4.353 0.000 . 92 7 7 G H3' H 4.644 0.000 . 93 7 7 G H4' H 4.344 0.000 . 94 7 7 G H5' H 4.097 0.000 . 95 7 7 G H5'' H 4.412 0.000 . 96 7 7 G H8 H 7.457 0.000 . 97 7 7 G C1' C 90.515 0.000 . 98 7 7 G C2' C 72.996 0.000 . 99 7 7 G C3' C 69.971 0.000 . 100 7 7 G C4' C 79.127 0.000 . 101 7 7 G C5' C 61.793 0.000 . 102 7 7 G C8 C 133.448 0.000 . 103 8 8 A H1' H 5.653 0.000 . 104 8 8 A H2 H 7.739 0.000 . 105 8 8 A H2' H 4.762 0.000 . 106 8 8 A H3' H 4.425 0.000 . 107 8 8 A H4' H 4.205 0.000 . 108 8 8 A H8 H 8.354 0.000 . 109 8 8 A C1' C 89.869 0.000 . 110 8 8 A C2 C 151.147 0.000 . 111 8 8 A C2' C 72.614 0.000 . 112 8 8 A C3' C 69.014 0.000 . 113 8 8 A C4 C 146.365 0.000 . 114 8 8 A C4' C 80.513 0.000 . 115 8 8 A C5 C 117.926 0.000 . 116 8 8 A C6 C 154.647 0.000 . 117 8 8 A C8 C 139.362 0.000 . 118 9 9 A H1' H 5.361 0.000 . 119 9 9 A H2 H 7.718 0.000 . 120 9 9 A H2' H 4.290 0.000 . 121 9 9 A H3' H 4.524 0.000 . 122 9 9 A H4' H 4.234 0.000 . 123 9 9 A H8 H 7.892 0.000 . 124 9 9 A C1' C 89.610 0.000 . 125 9 9 A C2 C 151.413 0.000 . 126 9 9 A C2' C 72.609 0.000 . 127 9 9 A C3' C 71.124 0.000 . 128 9 9 A C4 C 145.326 0.000 . 129 9 9 A C4' C 80.415 0.000 . 130 9 9 A C5 C 117.121 0.000 . 131 9 9 A C6 C 153.489 0.000 . 132 9 9 A C8 C 137.263 0.000 . 133 10 10 A H1' H 5.965 0.000 . 134 10 10 A H2 H 8.062 0.000 . 135 10 10 A H2' H 4.565 0.000 . 136 10 10 A H3' H 5.063 0.000 . 137 10 10 A H4' H 4.413 0.000 . 138 10 10 A H8 H 8.162 0.000 . 139 10 10 A C1' C 89.144 0.000 . 140 10 10 A C2 C 152.429 0.000 . 141 10 10 A C2' C 73.664 0.000 . 142 10 10 A C4 C 145.979 0.000 . 143 10 10 A C4' C 79.473 0.000 . 144 10 10 A C5 C 117.322 0.000 . 145 10 10 A C8 C 137.989 0.000 . 146 11 11 G H1' H 3.476 0.000 . 147 11 11 G H2' H 4.405 0.000 . 148 11 11 G H3' H 4.185 0.000 . 149 11 11 G H4' H 4.219 0.000 . 150 11 11 G H5' H 4.194 0.000 . 151 11 11 G H5'' H 4.321 0.000 . 152 11 11 G H8 H 7.830 0.000 . 153 11 11 G C1' C 90.048 0.000 . 154 11 11 G C2' C 71.625 0.000 . 155 11 11 G C3' C 71.482 0.000 . 156 11 11 G C4' C 79.967 0.000 . 157 11 11 G C5 C 116.014 0.000 . 158 11 11 G C5' C 66.824 0.000 . 159 11 11 G C8 C 134.532 0.000 . 160 12 12 A H1' H 5.933 0.000 . 161 12 12 A H2 H 7.725 0.000 . 162 12 12 A H2' H 4.321 0.000 . 163 12 12 A H3' H 4.578 0.000 . 164 12 12 A H4' H 4.403 0.000 . 165 12 12 A H5' H 4.018 0.000 . 166 12 12 A H5'' H 4.442 0.000 . 167 12 12 A H8 H 7.676 0.000 . 168 12 12 A C1' C 90.569 0.000 . 169 12 12 A C2 C 150.861 0.000 . 170 12 12 A C2' C 72.627 0.000 . 171 12 12 A C3' C 69.541 0.000 . 172 12 12 A C4 C 146.187 0.000 . 173 12 12 A C4' C 79.488 0.000 . 174 12 12 A C5 C 117.876 0.000 . 175 12 12 A C5' C 61.448 0.000 . 176 12 12 A C6 C 154.965 0.000 . 177 12 12 A C8 C 136.612 0.000 . 178 13 13 U H1' H 5.764 0.000 . 179 13 13 U H2' H 4.164 0.000 . 180 13 13 U H3' H 4.578 0.000 . 181 13 13 U H4' H 4.400 0.000 . 182 13 13 U H5 H 5.029 0.000 . 183 13 13 U H5' H 4.058 0.000 . 184 13 13 U H5'' H 4.500 0.000 . 185 13 13 U H6 H 7.490 0.000 . 186 13 13 U C1' C 88.386 0.000 . 187 13 13 U C2 C 150.257 0.000 . 188 13 13 U C2' C 72.924 0.000 . 189 13 13 U C3' C 72.251 0.000 . 190 13 13 U C4 C 165.346 0.000 . 191 13 13 U C4' C 81.646 0.000 . 192 13 13 U C5 C 100.853 0.000 . 193 13 13 U C5' C 63.278 0.000 . 194 13 13 U C6 C 139.306 0.000 . 195 14 14 G H1' H 5.928 0.000 . 196 14 14 G H2' H 4.865 0.000 . 197 14 14 G H3' H 4.839 0.000 . 198 14 14 G H4' H 4.520 0.000 . 199 14 14 G H5' H 4.145 0.000 . 200 14 14 G H5'' H 4.247 0.000 . 201 14 14 G H8 H 8.011 0.000 . 202 14 14 G C1' C 86.868 0.000 . 203 14 14 G C2' C 72.218 0.000 . 204 14 14 G C3' C 74.183 0.000 . 205 14 14 G C4 C 151.203 0.000 . 206 14 14 G C4' C 82.443 0.000 . 207 14 14 G C5 C 115.813 0.000 . 208 14 14 G C5' C 64.586 0.000 . 209 14 14 G C8 C 137.236 0.000 . 210 15 15 U H1' H 5.663 0.000 . 211 15 15 U H2' H 4.579 0.000 . 212 15 15 U H3' H 4.609 0.000 . 213 15 15 U H4' H 4.474 0.000 . 214 15 15 U H5 H 5.664 0.000 . 215 15 15 U H5' H 4.189 0.000 . 216 15 15 U H5'' H 4.422 0.000 . 217 15 15 U H6 H 7.979 0.000 . 218 15 15 U C1' C 90.821 0.000 . 219 15 15 U C2 C 150.376 0.000 . 220 15 15 U C2' C 73.037 0.000 . 221 15 15 U C3' C 70.552 0.000 . 222 15 15 U C4 C 166.417 0.000 . 223 15 15 U C4' C 80.513 0.000 . 224 15 15 U C5 C 100.881 0.000 . 225 15 15 U C5' C 62.750 0.000 . 226 15 15 U C6 C 140.825 0.000 . 227 16 16 C H1' H 5.532 0.000 . 228 16 16 C H2' H 4.283 0.000 . 229 16 16 C H3' H 4.501 0.000 . 230 16 16 C H4' H 4.428 0.000 . 231 16 16 C H5 H 5.615 0.000 . 232 16 16 C H5' H 4.078 0.000 . 233 16 16 C H5'' H 4.542 0.000 . 234 16 16 C H6 H 7.912 0.000 . 235 16 16 C C1' C 91.677 0.000 . 236 16 16 C C2 C 155.505 0.000 . 237 16 16 C C2' C 72.590 0.000 . 238 16 16 C C3' C 69.184 0.000 . 239 16 16 C C4 C 165.346 0.000 . 240 16 16 C C4' C 79.383 0.000 . 241 16 16 C C5 C 94.340 0.000 . 242 16 16 C C5' C 61.755 0.000 . 243 16 16 C C6 C 139.288 0.000 . 244 17 17 C H1' H 5.699 0.000 . 245 17 17 C H2' H 3.999 0.000 . 246 17 17 C H3' H 4.155 0.000 . 247 17 17 C H4' H 4.155 0.000 . 248 17 17 C H5 H 5.454 0.000 . 249 17 17 C H6 H 7.634 0.000 . 250 17 17 C C1' C 89.869 0.000 . 251 17 17 C C2 C 156.697 0.000 . 252 17 17 C C2' C 74.484 0.000 . 253 17 17 C C3' C 66.826 0.000 . 254 17 17 C C4 C 165.799 0.000 . 255 17 17 C C4' C 80.571 0.000 . 256 17 17 C C5 C 95.200 0.000 . 257 17 17 C C6 C 138.153 0.000 . stop_ save_